Calculating Coverage Allele Threshold Using .wig file

[jz...@tgen.org]

Dear Broad Institute,

As a follow-up from the last question, we want to be able to calculate the sum of mismatch qualities.  Is there a way to extract this information from a .wig file using igvtools to calculate the sum of mismatched base qualities and sum of all qualities?

Thank you so much,

Justin Zhu

[James Robinson]

Hi, no there is not.   igvtools is not an analysis package,  please don't try to use it to "call" snps,  you need a proper snp caller such as samtools or GATK to do this.   IGV is for visualization,  igvtools is to support visualization by compressing files.

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